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Crystallography Newsletter
Volume 8, No. 01, January 2016
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In this issue:


Rigaku Oxford Diffraction
invites all users of Rigaku equipment
to join us on our X-ray forum

Rigaku Oxford Diffraction forum screen

www.rigakuxrayforum.com

Here you can find discussions about software, general crystallography issues and more. It’s also the place to download the latest version of Rigaku Oxford Diffraction’s CrysAlisPro software for single crystal data processing.

We look forward to seeing you on there soon.


Rigaku Reagents: Wizard Classic crystallization screen series

Wizard Classic

www.rigakureagents.com

Rigaku Reagents' Wizard Classic screens were designed to increase the probability of producing crystals during the coarse screening crystallization trials of biological macromolecules. Wizard Classic screens offer a large range of crystallants, buffers, and salts covering a broad range of crystallization space at pH levels from pH 4.5 to pH 10.5. They are proven to be a highly effective starting point for screening, with non-repeating formulations. Each of these screens is offered in either a 96 deep well block plate format or in 10 ml tubes.


Survey of the month

Dec 2015 survey

survey



Video of the month

video

Some science boffins, 'mad professor' types, tell some great jokes! This video features a biologist, cosmologists, chemist, materials nano-chemist, science journalist, electronics engineer, professor of physics, evolutionary biologist, medical physicist, chemical biologist & a director of pure mathematics.

Our structural biology colleague, Prof. Lawrence Pearl, turns out to be quite the joke teller. His joke begins at 2:38.

video



Upcoming events

SPIE Advanced Lithography, February 21 – 25, 2016 in San Jose, CA, USA

60th Biophysical Society Meeting, February 27 – March 2, 2016 in Los Angeles, CA, USA

PITTCON, March 6 – 10, 2016 in Atlanta, GA, USA

See full list >


Last month's survey

After a long day in the lab, many of us have been known to head to the bar or pub to unwind in the company of others. If you are one of those people, what is your beverage of choice at the end of a hard day of research:

results


 

 

 

 

 

 

 

 

book cover

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Crystallography in the news

January 2, 2016. In Duchenne muscular dystrophy, mutations in the dystrophin gene can alter the structure and function of the protein. Researchers, led by Dr. Eric Olson, Chairman of Molecular Biology at The University of Texas Southwestern Medical Center, used the CRISPR gene-editing approach to permanently correct the DMD mutation that causes the disease in young mice.

January 6, 2016. Researchers used Diamond Light Source's latest innovation, a vacuum chamber for X-ray crystallography, to work out how some bacteria rip hydrogen apart to produce energy, just like a biological fuel cell. In the process they question the current ideas of how this happens and possibly move one step closer to a cheaper, more efficient, hydrogen economy.

January 8, 2016. Jean-Nicolas Longchamp of the University of Zurich, Switzerland, and his colleagues have imaged individual proteins using an electron holographic microscope, which uses interference patterns between electrons to produce an image.

January 15, 2016. Researchers have unveiled long-sought snapshots of the complex inner workings of nonribosomal peptide synthetases (NRPSs), megaenzymes that bacteria and fungi use to produce peptide-based natural products—including approved drugs such as the antibiotic vancomycin and the immunosuppressant cyclosporine.

January 18, 2016. Determining the crystal structures of biomolecules containing metal ions, such as metalloproteins, can be problematic as X-rays can damage the metals' surroundings, altering the molecules' structure. Kirill Gokhberg and coworkers at Germany's Heidelberg University have now teased apart the mechanism behind such radiation damage using computational methods. Their findings suggest that even fast X-ray methods could distort biomolecules.

January 18, 2016. Scientists at Cardiff University's School of Medicine have been able to explain why an experimental cancer therapy caused deaths; they used X-ray crystallography to understand how a modified T-cell receptor, which was intended to target a cancerous antigen, mistakenly began attacking healthy heart tissue.

January 19,2016. Dr. Olga Boudker, Associate Professor of Physiology and Biophysics at Weill Cornell Medical College, was named a Howard Hughes Medical Institute investigator for her work on a molecular machine called a glutamate pump. Dr. Boudker and her team were the first to use X-ray crystallography to capture atomic resolution snapshots of glutamate pumps as they work.

January 21, 2016. New research, from the Johns Hopkins University School of Medicine, that maps the 3D interactions of fluoroquinolones with the DNA machinery of the tuberculosis bacterium reveals clues that could help drug developers make these old anti-TB drugs more effective – even against resistant forms of the infectious lung disease.


Product spotlight: BioSAXS-2000

Rigaku's BioSAXS-2000 SAXS camera is designed specifically to meet the needs of the structural biologist. Based on a patented two-dimensional Kratky design, the BioSAXS-2000 takes up much less space than a conventional 3-pinhole camera but offers better flux characteristics. Best of all, the BioSAXS-2000 can be mounted on the open port of a Rigaku rotating anode X-ray generator, taking full advantage of existing infrastructure, or it can be mated to a Rigaku microfocus sealed tube X-ray source. The BioSAXS AUTO configuration incorporates two time-saving features: an Automatic Sample Changer for unattended overnight operation and an Automatic Analysis Pipeline based on the world standard ATSAS package from EMBL Hamburg.

BioSAXS-2000

Watch a new product video about the BioSAXS-2000.


Lab in the spotlight

Prof. Mark Glover Prof. Mark Glover
Department of Biochemistry
Faculty of Medicine & Dentistry
University of Alberta

The main focus of Mark Glover's research is to understand, in structural detail, the molecular processes by which gene expression and DNA repair are regulated. His lab uses a combination of biochemical and structural approaches to probe mechanistic aspects of several distinct systems.

Three specific areas of research include:

The DNA damage response and DNA repair
DNA damage response

Regulation of bacterial conjugation
regulation of bacterial conjugation

Regulation of eukaryotic gene expression
eukaryotic gene expression


Educational Corner: Ohad Medalia (University of Zürich) — Basic principle in three-dimensional electron microscopy

Ohad Medalia joined the Department of Biochemistry of University of Zurich in November 2010 as Associate Professor. He is an acknowledged expert in the field of cryo-electron tomography. His research focuses on macromolecular structures and mechanisms in eukaryotic cells, such as the integrin-mediated cell adhesion, the nuclear pore complex and the organization of nuclear lamin filaments.


Selected recent crystallographic papers

Dissecting the interface between apicomplexan parasite and host cell: Insights from a divergent AMA-RON2 pair. Parker, Michelle L.; Penarete-Vargas, Diana M.; Hamilton, Phineas T.; Guérin, Amandine; Dubey, Jitender P.; Perlman, Steve J.; Spano, Furio; Lebrun, Maryse; Boulanger, Martin J. Proceedings of the National Academy of Sciences of the United States of America. 1/12/2016, Vol. 113 Issue 2, p398-403. 6p. DOI: 10.1073/pnas.1515898113.

Identification of novel scaffolds for potential anti-Helicobacter pylori agents based on the crystal structure of H. pylori 3-deoxy-ᴅ-manno-octulosonate 8-phosphate synthase (HpKDO8PS). Cho, Sujin; Im, Hookang; Lee, Ki-Young; Chen, Jie; Kang, Hae Ju; Yoon, Hye-Jin; Min, Kyung Hoon; Lee, Kang Ro; Park, Hyun-Ju; Lee, Bong-Jin. European Journal of Medicinal Chemistry. Jan2016, Vol. 108, p188-202. 15p. DOI: 10.1016/j.ejmech.2015.11.036.

Kinetic and structural investigation of the cytokinin oxidase/dehydrogenase active site. Kopecný, David; Koncitíková, Radka; Popelka, Hana; Briozzo, Pierre; Vigouroux, Armelle; Kopecná, Martina; Zalabák, David; Šebela, Marek; Skopalová, Jana; Frébort, Ivo; Moréra, Solange. FEBS Journal. Jan2016, Vol. 283 Issue 2, p361-377. 17p. DOI: 10.1111/febs.13581.

Insights into open/closed conformations of the catalytically active human guanylate kinase as investigated by small-angle X-ray scattering. Jain, Rohit; Khan, Nazimuddin; Menzel, Andreas; Rajkovic, Ivan; Konrad, Manfred; Techert, Simone. European Biophysics Journal. Jan2016, Vol. 45 Issue 1, p81-89. 9p. DOI: 10.1007/s00249-015-1079-9.

In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures. Huang, Chia-Ying; Olieric, Vincent; Ma, Pikyee; Howe, Nicole; Vogeley, Lutz; Liu, Xiangyu; Warshamanage, Rangana; Weinert, Tobias; Panepucci, Ezequiel; Kobilka, Brian; Diederichs, Kay; Wang, Meitian; Caffrey, Martin. Acta Crystallographica Section D: Structural Biology. Jan2016, Vol. 72 Issue 1, p93-112. 19p. DOI: 10.1107/S2059798315021683.

Soft matter perspective on protein crystal assembly. Fusco, Diana; Charbonneau, Patrick. Colloids & Surfaces B: Biointerfaces. Jan2016, Vol. 137, p22-31. 10p. DOI: 10.1016/j.colsurfb.2015.07.023.

Structural Basis of Pullulanase Membrane Binding and Secretion Revealed by X-Ray Crystallography, Molecular Dynamics and Biochemical Analysis. East, Alexandra; Mechaly, Ariel E.; Huysmans, Gerard H.M.; Bernarde, Cédric; Tello-Manigne, Diana; Nadeau, Nathalie; Pugsley, Anthony P.; Buschiazzo, Alejandro; Alzari, Pedro M.; Bond, Peter J.; Francetic, Olivera. Structure. Jan2016, Vol. 24 Issue 1, p92-104. 13p. DOI: 10.1016/j.str.2015.10.023.

Structural Plasticity of the Protein Plug That Traps Newly Packaged Genomes in Podoviridae Virions. Bhardwaj, Anshul; Sankhala, Rajeshwer S.; Olia, Adam S.; Brooke, Dewey; Casjens, Sherwood R.; Taylor, Derek J.; Prevelige, Jr., Peter E.; Cingolani, Gino. Journal of Biological Chemistry. 1/1/2016, Vol. 291 Issue 1, p215-226. 12p. DOI: 10.1074/jbc.M115.696260.

A new default restraint library for the protein backbone in Phenix, a conformation-dependent geometry goes mainstream. Moriarty, Nigel W.; Tronrud, Dale E.; Adams, Paul D.; Karplus, P. Andrew. Acta Crystallographica Section D: Structural Biology. Jan2016, Vol. 72 Issue 1, p176-179. 3p. DOI: 10.1107/S2059798315022408.

Kinetic and structural studies reveal a unique binding mode of sulfite to the nickel center in urease. Mazzei, Luca; Cianci, Michele; Benini, Stefano; Bertini, Leonardo; Musiani, Francesco; Ciurli, Stefano. Journal of Inorganic Biochemistry. Jan2016, Vol. 154, p42-49. 8p. DOI: 10.1016/j.jinorgbio.2015.11.003.

Structure and functional roles of Epac2 (Rapgef4) . Sugawara, Kenji; Shibasaki, Tadao; Takahashi, Harumi; Seino, Susumu. Gene. Jan2016, Vol. 575 Issue 2 Part 3, p577-583. 7p. DOI: 10.1016/j.gene.2015.09.029.

Low resolution solution structure of an enzymatic active AhpC10:AhpF2 ensemble of the Escherichia coli Alkyl hydroperoxide Reductase. Kamariah, Neelagandan; Nartey, Wilson; Eisenhaber, Birgit; Eisenhaber, Frank; Grüber, Gerhard. Journal of Structural Biology. Jan2016, Vol. 193 Issue 1, p13-22. 10p. DOI: 10.1016/j.jsb.2015.11.004.

Nanostructured metal–organic frameworks and their bio-related applications. Giménez-Marqués, M.; Hidalgo, T.; Serre, C.; Horcajada, P. Coordination Chemistry Reviews. Jan2016 Part 2, Vol. 307, p342-360. 19p. DOI: 10.1016/j.ccr.2015.08.008.

Structural characterization of cevimeline and its trans-impurity by single crystal XRD. Stepanovs, Dmitrijs; Tetere, Zenta; Ravina, Irisa; Kumpinš, Viktors; Zicane, Daina; Bizdena, Erika; Bogans, Janis; Novosjolova, Irina; Grigalovica, Agnese; Meri, Remo Merijs; Fotins, Juris; Cerkasovs, Maksims; Mishnev, Anatoly; Turks, Maris. Journal of Pharmaceutical & Biomedical Analysis. Jan2016, Vol. 118, p404-409. 6p. DOI: 10.1016/j.jpba.2015.11.006.


Book review:

The Invention of Science: A New History of the Scientific Revolution

By David Wootton, HarperCollins Publishers, New York, 2015, 785 pages, ISBN: 978-0061759529.

We often think of invention as the product of scientific inquiry, but it doesn't seem as intuitively obvious to think of science itself as something that was invented. Yet that is exactly how David Wootton presents the history of the Scientific Revolution in his new book, The Invention of Science: A History of the Scientific Revolution.

Although it certainly isn't light reading, Wootton's newest work is jam-packed with information. It reads like a high-energy history textbook. Wootton sets out to provide "A New History of the Scientific Revolution," and certainly does so. He has found a way to reinvigorate this well-trodden tract of scientific history.

He opens with the claim "modern science was invented between 1572, when Tycho Brahe saw a nova, or new star, and 1704, when Newton published his Opticks, which demonstrated that white light is made up of light of all the colors of the rainbow." But despite this claim, Wootton, like any good historian, does not start at this proposed beginning, Brahe's observation of a nova, but rather with the first tool-making humans—2 million years ago. He gives a brief overview of the initial development of what might broadly be considered scientific progress in the early days of human civilization—nothing revolutionary, other than that it laid the groundwork for future innovations.

He then delves immediately into the Scientific Revolution of the 1600s—the revolution that he claims started with Brahe. It's important to keep in mind that when Wootton refers to science, he is not referring broadly to the many manifestations of human ingenuity, but rather the method of science, which he refers to as "the research programme" and "the experimental method." That is, science as a series of steps, starting with a hypothesis, developing an experiment to test it, doing the experiment, recording and analyzing the results, and repeating the process. The most important part of scientific discovery is reproducibility. If your results can't be reproduced, the theory or development you are proposing lacks the ability to be proven.

One of the statements I found most compelling in Wootton's book came in the last chapter: "science offers reliable knowledge (that is, reliable prediction and control), not truth." This is something we often forget about science, that it doesn't always offer us immovable truths about the world (and the universe) we live in, but it helps us understand it.

Review by Jeanette S. Ferrara
NYU School of Journalism

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